Troubles killings should be investigated chronologically, the Northern Ireland Secretary said.
Proposed new independent institutions considering deaths in an ordered manner will ensure outstanding probes into terrorist murders - including those of 185 soldiers - are followed up, James Brokenshire added.
Hundreds of veterans have marched on Downing Street protesting at what they believe is the "hounding" of troops who served in Northern Ireland.
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But prosecutors in Belfast revealed they had pursued five times more cases against alleged paramilitaries than servicemen in the past five years.
Mr Brokenshire said: "The proposed new institutions, set out in the Stormont House Agreement, have a number of important advantages over the system currently in place in Northern Ireland, including that they will consider deaths in chronological order.
"This will ensure that outstanding investigations into terrorist murders, including the murder of 185 soldiers, are investigated and evidential leads are pursued."
Retired soldier Dennis Hutchings, 75, has been charged with attempted murder over a fatal shooting in 1974.
Two other former soldiers are facing prosecution for murder over the 1972 death of Joe McCann, an official IRA commander.
The Police Service of Northern Ireland (PSNI) investigates legacy cases in an order based on whether they involve individuals who may cause harm today, those with forensic potential and those where no individual has been charged and convicted of the primary offence, a PSNI document explains.
One third of cases which Northern Ireland's director of public prosecutions has referred to detectives to investigate relate to Troubles incidents involving security force members.
The 2014 Stormont House Agreement between the British and Irish Governments and the main Stormont parties decided an independent Historical Investigations Unit (HIU) should be established to review cases.
It has been stalled as part of the wider political malaise which has threatened powersharing in Northern Ireland.
In a parliamentary statement, Mr Brokenshire said: "I am concerned that the existing mechanisms for investigating incidents which occurred during the Troubles are disproportionately focused on the actions of the Armed Forces and former police officers, rather than the terrorists who were responsible for 90 per cent of deaths.
"This is wrong and it has to change.
"That is why this Government supports the full and faithful implementation of the Stormont House Agreement, which would see a move to a new system that would, under legal obligations, operate in ways that are fair, balanced and proportionate."